Cont: The One Covid-19 Science and Medicine Thread Part 4

[marting]

Genetic association for asymptomatic and long covid

Good piece by Eric Topol going through a new Nature paper where strong genetic associations were found for asymptomatic covid. Also a preprint showing strong associations with long covid. Very promising. Especially for possible ways to treat/prevent long covid.

https://erictopol.substack.com/p/from-asymptomatic-covid-to-long-covid

In the Nature paper by Jill Hollenbach and colleagues, 3 cohorts were assessed. The discovery group was from a smartphone-app study tracking Covid symptoms and outcomes (“Citizen Science”) for nearly 30,000 participants (over 1,400 asymptomatic with a positive test). Confirmation was obtained in two other cohorts that an immune function human leukocyte antigen (HLA) locus—HLA-B*15:01—was strongly associated with lack of developing symptoms.

 

[The Atheist]

Devastating COVID-19 surge in Okinawa exposes lies that the pandemic is over (WSWS.org, July 8, 2023)

I'm surprised you and your pals at World Socialist Web haven't been posting more about this "devastating" covid wave in Japan. Things must be truly horrific there now with arcturuskrakenbaloney attacking so hard.

Could it be that it's just another fizzer overblown by panic-merchants? Two weeks since your post and all I hear are crickets. (hospitalisations in Okinawa are down by 20% in the last week, btw - hysterically referred to as "down slightly".)

Good piece by Eric Topol going through a new Nature paper where strong genetic associations were found for asymptomatic covid. Also a preprint showing strong associations with long covid. Very promising. Especially for possible ways to treat/prevent long covid.

https://erictopol.substack.com/p/from-asymptomatic-covid-to-long-covid

Bloody interesting, and confirms what was thought a couple of years back.

Now, if we can just identify these things a whole lot earlier in the pandemic...

 

[dann]

As for "this "devastating" covid wave in Japan," I assume this is what The Atheist has been looking for but couldn't find:

COVID-19 cases in Japan are continuing their recent rise and taking a toll on the elderly in particular, with experts predicting the trend will continue amid high heat, declining population-level immunity and the start of the holiday season.
Health ministry statistics released Friday showed Japan’s ninth wave of coronavirus infections is continuing, with the average number of new cases reported by around 5,000 designated medical institutions in the week through July 9 standing at 9.14, up from 7.24 a week before.
Japan has seen a continuous, though gradual, increase in COVID-19 cases for eight straight weeks since May 8, when it downgraded the disease to a status on par with seasonal flu and scrapped a range of special COVID-19 measures, including the daily counting of cases.
The number of new hospital admissions for COVID-19 is also rising, standing at 6,096 in the week through July 9, up from 5,494 a week before and 4,484 four weeks before.
Rise in new COVID-19 cases in Japan shows little sign of abating (Japan Times, July 18, 2023)

So, yeah, pretty devastating, in particular if one doesn't consider its impact on the elderly to be irrelevant.

As for the "arcturuskrakenbaloney attacking so hard":

He [Shigeru Omi, the nation’s top coronavirus adviser] also mentioned the fact that many people’s immunity is waning, as time has passed since prior infection or vaccination, as well as the prevalence of immunity-escaping variants.

As for my alleged "pals at World Socialist Web":
As ninth COVID wave sweeps Japan, wastewater data show another surge beginning in the US (WSWS, July 16, 2023)
US flying blind amid warnings of new COVID-19 surge (WSWS, July 17, 2023)

And finally, as for "Two weeks since your post and all I hear are crickets."
I post when I post. There is no reason to wait impatiently for my next post. If "hospitalisations in Okinawa are down by 20% in the last week," that's good, in particular if it is not because "the emergency center has had to limit new patients because all its beds are taken." (Asahi Shimbun, July 1, 2023). I hope that the numbers are down because local measures against the surge are effective.

 

[dann]

The Atheist's herd-immunity-by-infection recommendation:

Some people are going to lose their **** over that.

It's a good reason to not get booster shots, because we know the protection against severe disease does last, so you're better to let the disease take its course and build up personal and herd immunity.

I'm quite amused by it.

It has been two weeks since marting's very different conclusion, but only two days since The Atheist's latest post. Maybe he just didn't see it.

As for TA's comment, I have chosen to get boosters but am not going to double up on the bi-valent. I expect to get the new mono booster as soon as it becomes available absent newer negative data. From the data I've seen it appears to materially broaden antibody response.

 

[The Atheist]

It has been two weeks since marting's very different conclusion, but only two days since The Atheist's latest post. Maybe he just didn't see it.

No, the science is changing, and if a useful vaccine is available, like Marting, I will get one and recommend others do.

Do keep up, there's a good chap.

 

[Dr.Sid]

As wolrdometer and ourworldindata are useless recently for covid tracking, here are some sources for Japan:

Very simple, but good for overview - Mainichi news: https://mainichi.jp/english/covid19
Very detailed, CSV for download, but no useful way to visualize them - ministry of health: https://www.mhlw.go.jp/stf/covid-19/kokunainohasseijoukyou_00006.html

 

[marting]

Association between nose picking and SARS-CoV-2 incidence

Why not to pick your nose: Association between nose picking and SARS-CoV-2 incidence, a cohort study in hospital health care workers

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288352#pone-0288352-g001

SARS-CoV-2 incidence was higher in nose picking HCW compared to participants who refrained from nose picking (32/185: 17.3% vs. 2/34: 5.9%, OR 3.80, 95% CI 1.05 to 24.52), adjusted for exposure to COVID-19. No association was observed between nail biting, wearing glasses, or having a beard, and the incidence of SARS-CoV-2

 

[The Atheist]

Makes sense! Pretty funny study.

 

[Skeptic Ginger]

The weird thing about that nose picking, I was in the clinic Monday and I watched this guy pick his nose then casually wipe it on the side of the chair he was sitting in. Ewwwww.

I wanted to share what I saw but how do you bring that up in casual conversation?

 

[rjh01]

Why not to pick your nose: Association between nose picking and SARS-CoV-2 incidence, a cohort study in hospital health care workers

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288352#pone-0288352-g001

SARS-CoV-2 incidence was higher in nose picking HCW compared to participants who refrained from nose picking (32/185: 17.3% vs. 2/34: 5.9%, OR 3.80, 95% CI 1.05 to 24.52), adjusted for exposure to COVID-19. No association was observed between nail biting, wearing glasses, or having a beard, and the incidence of SARS-CoV-2

Here is a useful tip for any researchers. Measure the relationship between at least 20 activities, such as nose picking and Covid 19. You will find a relationship with > 95% probability with at least one of them. You then publish your results. Just do not mention the other 19 potential relationships you measured. If future researches fail to duplicate this relationship say they have not done the experiment properly.

 

[Skeptic Ginger]

Here is a useful tip for any researchers. Measure the relationship between at least 20 activities, such as nose picking and Covid 19. You will find a relationship with > 95% probability with at least one of them. You then publish your results. Just do not mention the other 19 potential relationships you measured. If future researches fail to duplicate this relationship say they have not done the experiment properly.

You have evidence of this theory or did it just sound good when it came to you?

 

[jt512]

Here is a useful tip for any researchers. Measure the relationship between at least 20 activities, such as nose picking and Covid 19. You will find a relationship with > 95% probability with at least one of them. You then publish your results. Just do not mention the other 19 potential relationships you measured. If future researches fail to duplicate this relationship say they have not done the experiment properly.

You have evidence of this theory or did it just sound good when it came to you?

He's right. It's p-hacking 101. The probability of a false positive conventional significance test is 0.05. He's provided a succinct explanation of the essence of the reproducibility crisis.

 

[dann]

No, the science is changing, and if a useful vaccine is available, like Marting, I will get one and recommend others do.

Do keep up, there's a good chap.

It's not so not science changing. It's the virus changing, which you would know if you were a good chap and kept up.
I guess it's progress that you now seem to at least understand that vaccine is useful. Maybe you have even realized that getting infected isn't.

Some people are going to lose their **** over that.
It's a good reason to not get booster shots, because we know the protection against severe disease does last, so you're better to let the disease take its course and build up personal and herd immunity.
I'm quite amused by it.

By the way, the new "variant of interest" is called Eris, so I'll help you keep up instead of having you spread the usual antivax, natural-immunity-by-infection disinformation:

He [Eric Topol] said the updated boosters will be better aligned against the viruses circulating now than the current formula targeting the BA.5 subvariant that became dominant in summer 2022.
What to know about EG.5, the most prevalent covid subvariant in the U.S. (WP, Aug 9, 2023)

 

[angrysoba]

Here is a useful tip for any researchers. Measure the relationship between at least 20 activities, such as nose picking and Covid 19. You will find a relationship with > 95% probability with at least one of them. You then publish your results. Just do not mention the other 19 potential relationships you measured. If future researches fail to duplicate this relationship say they have not done the experiment properly.

You have evidence of this theory or did it just sound good when it came to you?

He's right. It's p-hacking 101. The probability of a false positive conventional significance test is 0.05. He's provided a succinct explanation of the essence of the reproducibility crisis.

Assuming that that is how this particular study was done. (there are some other behaviours such as glasses-wearing, nail-biting and beard-wearing that are also included).

By now, this is such a well-known practice that it would be pretty risky to brazenly assert that anyone not replicating their findings were simply incompetent.

Usually, studies such as this would be pre-registered (not sure if that is the case here) with it being specific about what outcomes are being looked for).

I do notice though that this paper is open-source including the peer-review which is something that makes me trust the paper more.

 

[dann]

As wolrdometer and ourworldindata are useless recently for covid tracking, here are some sources for Japan:

Very simple, but good for overview - Mainichi news: https://mainichi.jp/english/covid19Very detailed, CSV for download, but no useful way to visualize them - ministry of health: https://www.mhlw.go.jp/stf/covid-19/kokunainohasseijoukyou_00006.html

Still rising.
Transition of patient numbers per medical facility (nationwide) now at more than 50% of the most recent peak in December-January.
And Japan is not the only country where numbers are rising:

2) Italy COVID deaths are increasing again - 2.5x in 2 weeks, as pointed out by
@Antonio_Caramia
. Have to see if this continues.
Eric Feigl-Ding (Twitter, Aug 11, 2023)

5) the signals are all going in the wrong direction. The doubling of #COVID ICU hospitalizations in New York is quite shocking to be honest.
Eric Feigl-Ding (Twiter, Aug 12, 2023)

As a side node, I show you Berlin waste water monitoring data, note the exponential y-axis.
~~ factor 7 within 1 month
Dominik Lenné (Twitter, Aug 11, 2023)

If proper testing was still being done, we would know more - and sooner - but alas ...

For graphs and numbers, go to the tweets.

 

[dann]

... (there are some other behaviours such as glasses-wearing, nail-biting and beard-wearing that are also included). ...

A Danish group studied the effect of wearing glasses:

Folk uden briller havde fire gange højere risiko for at blive smittet i nyt dansk studie, der får ros af professor.
Overraskende studie: Briller beskytter muligvis mod corona (Videnskab.dk, Nov 3, 2022)

People without glasses had a four times higher risk of getting infected according to a new Danish study lauded by a professor.
Surprising study: Glasses may offer protection from coronavirus

"Your bad eyesight may have protected you from coronavirus"

However, a Norwegian study didn't find a significant effect: Glasses Against transmission of SARS-CoV-2 in the community (GLASSY): a pragmatic randomized trial (preprint).

 

[zooterkin]

Flu and Covid boosters only available on the NHS to over-65s and those at greater risk this winter in the England. Last year, both were available to over-50s. You can pay for a flu jab, but you can't buy a Covid jab in the UK.

https://www.theguardian.com/society...s-to-under-65s-amid-fears-for-nhs-this-winter

 

[marting]

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288352#pone-0288352-g001

SARS-CoV-2 incidence was higher in nose picking HCW compared to participants who refrained from nose picking (32/185: 17.3% vs. 2/34: 5.9%, OR 3.80, 95% CI 1.05 to 24.52), adjusted for exposure to COVID-19. No association was observed between nail biting, wearing glasses, or having a beard, and the incidence of SARS-CoV-2

I'm most annoyed by the rigid adoption of p-value as determinative of whether there is an association or not. This study is a prime example. The p-values of nose picking and wearing glasses are extremely close to .05 with nose picking slightly lower and wearing glasses slightly higher. This can be seen from the CIs.

Nose picking: AdjOR 3.8 (1.05 - 24.52) p is barely below .05
Wearing glasses: AdjOR .49 (.23 - 1.06) p is barely above .05

What's funny is that the numbers are so close that the unadjusted ORs flip the significance with nose picking not being significant and wearing glasses significant. I'm sure they were careful to set the "adjustment" methodology in advance. Wouldn't want to go p-hacking.

This is why people need to read the paper and not just scan the words in the abstract.

 

[Skeptic Ginger]

He's right. It's p-hacking 101. The probability of a false positive conventional significance test is 0.05. He's provided a succinct explanation of the essence of the reproducibility crisis.

Then why did at least one of the controls, nail biting, not show the same correlation?

We did not find an association between nail biting and the incidence of SARS-CoV-2 infection. This might be explained by the protective effects of salivary proteins which were recently demonstrated to inhibit SARS-CoV-2 spike protein binding to the ACE2 receptor [30], making the mouth merely an exit rather than an entrance route for viral transmission [24].

In addition the study is supported by the hypothesis the nose is a portal of entry, especially if directly inoculated.

And multiple past studies have shown doctors don't was their hands as often as infection control guidelines require. Here's one of many found with an easy search:
Why don't doctors wash their hands? A correlational study of thinking styles and hand hygiene.

One might find, however that the correlation is explained by hand hygiene rather than nose picking. And, I agree like all of these studies, it needs to be repeated, something we never do enough of.

Dismissing the results with casual handwaving suggests the researchers were stupid and I doubt they were.

 

[Skeptic Ginger]

A Danish group studied the effect of wearing glasses:

People without glasses had a four times higher risk of getting infected according to a new Danish study lauded by a professor.
Surprising study: Glasses may offer protection from coronavirus...

However, a Norwegian study didn't find a significant effect: Glasses Against transmission of SARS-CoV-2 in the community (GLASSY): a pragmatic randomized trial (preprint).

So many of these studies fail to be repeatable. It's a huge problem with medical research. Few researchers want to revisit topics already investigated.